利用 ISIS Draw 繪製 2D 化學結構

利用ISIS Draw繪製2D化學結構 Ta-Wei Li NCTU

Today’s Job • Practice ISIS Draw Basic • Aromatic Compounds • Basic Aliphatic Compounds • Draw 2D Chemical Structure • Draw 2/3D Chemical Structure

Basic Strategy for ISIS Draw (1) • All atoms are carbons unless you specify otherwise. • Click benzene of the template-tool icons on the horizontal tool bar: • To place this template anywhere, just click an empty area.

Basic Strategy for ISIS Draw (2) • Click benzene Icon again • Then move the mouse to one bond of the previous benzene • Click the bond • After attachment, one can obtain naphthalene molecule

Select, Copy and Paste • Click the 「Select」 tool that appears on the tool bar • Understand the difference among • Then, move the mouse to naphthalene • Click the mouse and circle naphthalene like • Select “Edit”“Copy” and “Edit”“Paste” • Move the 2nd naphthalene to a empty space

Resizing Structures • To resize a structure, select it, then drag one of the corner handles • To scale a structure, select it, and then choose Object > Scale > Percent. Enter a number - without a % sign - to scale the structure.

Rotate Molecule – 2D & 3D • Click the 「2D Rotate」 tool that appears on the tool bar • Understand the difference between • Click the mouse to select one of two naphthalene molecules, like • Try to rotate the selected molecule in 2D direction or 3D direction

Drawing Bonds • To draw bonds, click a bond tool on the tool bar, such as • Then move the mouse to any atom of the 2nd naphthalene, such as • Click the mouse to sprout a bond from a atom • Keep adding a bond to every atom (except two bridge atoms)

Drawing Atoms • To draw an atom, click • Then move the mouse to any sprouted bond of the 2nd naphthalene, such as • Click the mouse • See a text entry field and choose H from a list

Deleting atoms, bonds, and structures • Select one or more atoms, bonds, or structures. Then, do one of the following: • Press the Delete key. • Choose Edit > Cut. • To delete atoms or bonds one at a time, click , then click an atom or bond.

Change Bond Type • Click benzene Icon again • Click any empty area to get benzene • Use right mouse button to click one bond and select “Edit Bond” • In the folder of “Bond”, please select “Single/Aromatic” to get 1.5 bond drawn as the down right figure

Generate Chemical Names • Draw a chemical compound as the right pictures • Select the whole molecule • Click on

Automatically Create H Atoms • Select p-Xylene and click on the right button of the mouse • Select “Edit Molecule…” • On the “Atom” Folder, Select “Auto position” to create the H atoms automatically.

ISIS Draw Practice 1 • Please draw following molecular structures (20%)

ISIS Draw Practice 2 • Please draw the line structures of the following three molecule and show their molecular formulas and IUPAC names (30%)

Express Moles and Charges • Press • Type 「H2SO4」 • Type 「H+」 • Type「SO42-」 ?

Use Superscript to Express Charge • Press • Type SO4\S2-\S • \S : superscript. You must use a capital S.

Express Free Radical and Isotope • Press • Type 「Cl.」 • Type 「15O」

Draw Alkane, Alkene, Alkyne (1) • To draw bonds, press a bond tool on the tool bar, such as • Next, drag the mouse onto the double-bond tool • Release the mouse and the cursor indicates that you can draw double bonds

Draw Alkane, Alkene, Alkyne (2) • To place this double bond anywhere, just click an empty area and then drag the mouse for the direction of the bond • Click and move the mouse to any end of the double bond • See a text entry field and type CH2 • Do the same input to another end of the double bond to get

Draw Alkane, Alkene, Alkyne (3) • With the choice of , move the mouse to the double bond area, such as • Click once to get • Click twice to get

Explicitly Show C atom of CO2 • First draw • Then change single bonds into double bonds • Add C atom in the center of CO2 molecule • Click • Click the center of CO2, select “more” • In “Symbol” of the “Atom” folder, select “C(show)” to show C atom explicitly

Clean CO2 molecule • Add O atoms in the two ends of CO2 as • Select the whole CO2 molecule • Click “Object”“Clean Molecule” to get the proper molecular model of CO2

Sprout Hydrogen • To draw chain molecules, click a chain tool on the tool bar, such as • Select the whole molecule • Click 「Object」「Edit Molecule」 • In 「Hydrogen」of「Atom」folder, select 「Auto position」

Draw Vitamin K (1) • To draw chain molecules, click a chain tool on the tool bar, such as • Click an empty area and then drag until a 10-atom chain appears • Move the mouse to the 4thatom and click it to sprout a bond, such as • Move the mouse to the 8thatom and click it to sprout a bond, such as

Draw Vitamin K (2) • Move the mouse to the 3rdbond and click it to create a double bond, such as • Click and move the mouse to the 10th atom, and then type H, such as • Question 1 : What should be the groups in the two red squares?

Draw Vitamin K (3) • Click and move the mouse to the left corner above of 6th atom such as • Click there as the start point of a bracket and drag the mouse to the right corner below • Chose “multiple group” in Bracket type and type “3” in Repeat count • Click “Apply” and close the window to get

Draw Vitamin K (4) • Please finish the following picture

Chemistry Information of Vitamin K • Select 「Vitamin K」 molecule • Then select 「Chemistry」「Calculate Mol Values」「Calculate」to show the chemistry information of Vitamin K • Molecular Weight • Molecular Formula • Molecular Composition

ISIS Draw Practice 3 • Please draw and clean the molecular structure of Vitamin K, and then show its molecular information including molecular weight and molecular formula. (10%) • Please draw the line structures of the following two molecule and show their molecular formulas and IUPAC names (10%)

Draw 2/3D Chemical Structure (1) • Click • Click an empty area as the start point and then drag until a 4-atom chain appears • Click the rotation tool • Click any part of the molecule and drag the mouse to rotate the molecule, such as

Draw 2/3D Chemical Structure (2) • Click the up-wedge tool • Click the 2nd atom and drag the up-wedge bond to the correct direction, such as • implies the bond above the molecular plane

Draw 2/3D Chemical Structure (3) • Press and drag the mouse to the down-wedge tool • Click the 2nd atom and drag the down-wedge bond to the right direction, such as • implies the bond below the molecular plane

Draw 2/3D Chemical Structure (4) • Click the down-wedge bond again to change its direction from to • Please finish the following picture

Draw Cyclohexane (1) • Click cyclohexane of the template-tool icons on the horizontal tool bar • Click an empty area and click the rotation tool to rotate cyclohexane to get • Select the up-wedge tool and click cyclcohexane to get

Draw Cyclohexane (2) • Select the up-bond tool • Click the Cyclohexane to get

Draw Cyclohexane (3) • Click “Templates”“Rings” • Among various rings, click • Please try to finish the following picture

ISIS Draw Practice 4 • 請畫出 CH2CCCCH2 化合物的 2/3D 的結構圖。(10%) • 請畫出下列化合物的順式2/3D結構圖。(10%)

ISIS Draw Practice 5 • Please draw following molecular structures (10%)

ISIS Draw Homework • Finish ISIS Draw practice 1, 2, 3, 4, and 5, and save the file as “ isisHW.skc ” • 請在今天（2月24日）午夜十二點將 “isisHW.skc”上傳至 http://bb.nctu.edu.tw • 2月24日午夜十二點以前繳交，滿分為100分 • 3月3日午夜十二點以前繳交，滿分為80分 • 3月3日午夜十二點以後就不需要繳交，以0分計算

利用 ISIS Draw 繪製 2D 化學結構